I just reset back to a fresh install of OS X Lion, and came upon this Gephi error.

To fix:
Make sure /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK is symbolically linked to the custom/downloaded JDK (/Library/Java/JavaVirtualMachines/1.6.0_30-b12-409.jdk/Contents for me)
Open Java Preferences in Applications/Utilities, and pull 32-bit Java in front of 64-bit Java.